Quantitative analysis of disease associated mutations and sequence variants

Abstract: A solid-phase sequencing technique was applied to quantify the mitochondrial A3243G mutation in three families with maternally inherited diabetes and deafness. A correlation between the level of heteroplasmy and age at onset was found. The fluctuation of the heteroplasmy levels of the A3243G mutation was monitored from 4 to 18 years, in three female patients. Using the minisequencing method, the level of heteroplasmy was found to decrease over time in endothelial cell samples from all three patients. With a similar strategy, the heteroplasmy levels of two neutral polymorphisms in the non-coding region of the mtDNA in healthy individuals were monitored. It has recently been suggested that heteroplasmy occurs frequently at neutral nucleotide positions in the control region of mtDNA and that the heteroplasmy level changes with age. The level of heteroplasmy of the neutral polymorphisms was found to remain unchanged over a time period of up to 25 years in four individuals. Wilson disease (WD) is caused by mutations in the ATP7B gene that encodes a mitochondrial copper-transporting ATPase. The worldwide prevalence of WD has been estimated to 1 in 30 000. Based on the number of diagnosed patients the estimated prevalence in the Swedish population would be 1 in 300 000. The prevalence of WD in Sweden was estimated indirectly by quantitative minisequencing analysis of two WD-causing mutations in pooled DNA samples. In addition, the population frequencies of eight SNPs in the ATP7B gene were determined. Our results confirmed that WD is truly more rare in Sweden than in other populations. A previously nondetectable diversity of alleles at the KIT locus, determining the coat color of pigs, was found by using three quantitative methods, minisequencing, pyrosequencing and the "TaqMan" 5' exonuclease assay. A splice-site mutation and a duplication of the KIT gene, encoding the mast/stem cell growth factor receptor causes the allelic diversity. Despite of a strong selection for white color dating from the medevial era, the desired phenotype has not been fixed. This study provides tools for genotyping the complicated KIT locus in pigs, which may be used for the purpose of breeding true for white color.